The removal of biomolecules from medical instruments by plasma could be a difficult task due to the fact that many medical instruments are made of polymers, which can be etched in plasma as well. The etching rates of selected blood proteins, platelet‐poor plasma (PPP) and polymer polyethylene terephthalate (PET) were studied. In the case of blood proteins, fibrinogen (FIB) and human serum albumin (HSA) were used. Films of PPP, FIB, HSA and PET were deposited on the quartz crystals and exposed to oxygen atoms in early and late afterglow of microwave plasma at different pressures between 50 and 400 Pa. The thickness of the films versus etching time was measured by quartz crystal microbalance. The thickness of PET film decreased linearly with etching time, while the thickness of both protein films and PPP decreased exponentially with time. In all cases, the etching rates were first increasing with the increasing pressure, while later they reached a constant value. Furthermore, the etching rates were higher in the early afterglow than in the late afterglow. The etching rates of PPP were higher than the etching rates of both proteins HSA and FIB. The slowest etching rate was observed for PET polymer, where the etching rate was lower by two orders of magnitude in comparison to both proteins and PPP. Copyright © 2014 John Wiley & Sons, Ltd.